Use a data class to store morphological parameters of a cell.

RunExample.m

@@ -135,32 +135,17 @@ max_z = max( z_junction );
 z_junction = max_z -  z_junction;
 junction_graph.Nodes.Centroid = [ junction_graph.Nodes.Centroid z_junction ];
 
-for i = 1 : n_objects    
+for i = 1 : n_objects
     objects( i ).boundary( :, 3 ) = max_z - objects( i ).boundary( :, 3 );
     objects( i ).center( 3 ) = max_z - objects( i ).center( 3 );
 end
 
-%% Compute object de-projected area.
+%% Create epicell instances.
 
-for i = 1 : n_objects
-    
+epicells = repmat( epicell, n_objects, 1 );
+for i = 1 : n_objects    
     o = objects( i );
-    
-    [ area, uncorr_area ] = area3d( o );
-    [ perim, uncorr_perim ] = perimeter3d( o );
-    [ f, E ] = fit_ellipse( o );
-    
-    objects( i ).id = i;
-    objects( i ).area = area;
-    objects( i ).perimeter = perim;
-    objects( i ).euler_angles = E;
-    objects( i ).ellipse_fit = f;
-    
-    uncorr = struct();
-    uncorr.area = uncorr_area;
-    uncorr.perimeter = uncorr_perim;
-    objects( i ).uncorr = uncorr;
-    
+    epicells( i ) = epicell( o.boundary, o.junctions, i  );
 end
 
 
@@ -200,7 +185,7 @@ axis equal
 
 for i = 1 : n_objects
     
-    o = objects( i );
+    o = epicells( i );
     P = o.boundary;
     
     %     err = o.perimeter / o.uncorr.perimeter - 1;

src/area3d.m

-function [ area, uncorr_area ] = area3d( o )
-%AREA3D Computes the area of the object.
-    
-    %% Deprojected 3D version.
-    
-     % Put all vertex coordinates with respect to center.
-    p = centered_points( o );
-
-    n_vertices = size( p, 1 );
-
-    % Build small triangles.
-    index = [ 2 : n_vertices 1 ];
-    p1 = p;
-    p2 = p( index, : );
-    
-    % Cross product.
-    cp = cross( p1, p2 );
-    
-    % Norm of each vector.
-    vn = euclidean_norm( cp );
-    
-    % Positive area.
-    area_triangle = abs( vn );
-
-    % Total positive area.
-    area = sum( area_triangle ) / 2;
-    
-    %% 2D area.
-    
-    uncorr_area = polyarea( o.boundary(:,1), o.boundary(:,2) );
-    
-    
-    %% Subfunction.
-    
-    function n = euclidean_norm( v )
-        n = sqrt( sum( v .* v, ndims( v ) ) );
-    end
-
-end
-

src/centered_points.m

-function p = centered_points( o )
-%CENTERED_POINTS Returns the 3D coordinates of the object bounds, with
-%respect to its center.
-
-    p = o.boundary;
-    n_vertices = size( p ,1 );
-    center = mean( p );
-    center = repmat( center, [ n_vertices, 1 ] );
-    p = p - center;
-
-end
-

src/epicell.m

+classdef epicell
+    %EPICELL Data class that store data resulting from tissue cell segmentation.
+    
+    % Immutable class: all properties are read-only.
+    properties (SetAccess = private)
+        boundary
+        center
+        junction_ids
+        area
+        perimeter
+        euler_angles
+        ellipse_fit
+        uncorrected_area
+        uncorrected_perimeter
+        id
+    end
+    
+    methods
+        function obj = epicell( boundary, junction_ids, id )
+            %EPICELL Construct an epicell from a N x 3 list of points.
+            
+            if nargin == 0
+                return
+            end
+            
+            % Base properties.
+            obj.boundary = boundary;
+            obj.junction_ids = junction_ids;
+            obj.id = id;
+            obj.center = mean( boundary );
+            
+            % Morphological descriptors.
+            p = epicell.centered_points( boundary );
+            [ obj.area, obj.uncorrected_area ] = epicell.area3d( p );
+            [ obj.perimeter, obj.uncorrected_perimeter ] = epicell.perimeter3d( p );
+            obj.euler_angles = epicell.fit_plane( p );
+            obj.ellipse_fit = fit_ellipse( p, obj.euler_angles );            
+        end
+    end
+    
+    %% Static methods: compute final properties value.
+    methods ( Access = private, Hidden = true, Static = true )
+        
+        function p = centered_points( p )
+            %CENTERED_POINTS Returns the 3D coordinates of the object bounds, with
+            %respect to its center.
+            n_vertices = size( p ,1 );
+            center = mean( p );
+            center = repmat( center, [ n_vertices, 1 ] );
+            p = double( p - center );
+        end
+        
+        function [ area, uncorr_area ] = area3d( p )
+            %AREA3D Computes the area of the object.
+            
+            n_vertices = size( p, 1 );
+            
+            % Build small triangles.
+            index = [ 2 : n_vertices 1 ];
+            p1 = p;
+            p2 = p( index, : );
+            
+            % Cross product.
+            cp = cross( p1, p2 );
+            
+            % Norm of each vector.
+            vn = euclidean_norm( cp );
+            
+            % Positive area.
+            area_triangle = abs( vn );
+            
+            % Total positive area.
+            area = sum( area_triangle ) / 2;
+            
+            % 2D area.
+            uncorr_area = polyarea( p(:,1), p(:,2) );
+            
+            function n = euclidean_norm( v )
+                n = sqrt( sum( v .* v, ndims( v ) ) );
+            end
+            
+        end
+        
+        function [ perim, uncorr_perim ] = perimeter3d( p )
+            %PERIMETER3D Perimeter of a closed N-dimensional polygon.
+            
+            perim = compute_perim( p );
+            uncorr_perim = compute_perim( p( : , 1:2 ) );
+            
+            function l_perim = compute_perim( p )
+                % p can be a N x d matrix, with d being the dimensionality.
+                
+                p2 = [ p ; p( 1, : ) ];
+                p_diff = diff( p2 );
+                
+                p_diff_2 = p_diff .* p_diff;
+                p_diff_2_sum  = sum( p_diff_2, 2 );
+                sls = sqrt( p_diff_2_sum );
+                l_perim = sum( sls );
+            end
+        end
+        
+        function E = fit_plane( p )
+            % Fit a plane to these points.
+            [ ~, ~, v ] = svd( p );
+            E = rot2eulerZXZ( v );
+        end
+    end
+end
+

src/fit_ellipse.m

-function [ f, E ] = fit_ellipse( o )
+function f = fit_ellipse( p, E )
 %FIT_ELLIPSE Fit a 2D ellipse to the 3D points.
 %   The fit requires the Euler angles of the plane fitted through the
 %   opints, so that we can project them on this plane. We then make a 2D 
@@ -8,11 +8,12 @@ function [ f, E ] = fit_ellipse( o )
 %   Greatly inspired from 
 % https://stackoverflow.com/questions/29051168/data-fitting-an-ellipse-in-3d-space
 
-     p = double( centered_points( o ) );
-    
     % Fit a plane to these points.
-    [ ~, ~, v ] = svd( p );
-    E = rot2eulerZXZ( v );
+    if nargin < 2
+        [ ~, ~, v ] = svd( p );
+    else
+        v = euleurZXZ2rot( E );
+    end
     
     % Rotate the points into the principal axes frame.
     p = p * v;

src/perimeter3d.m

-function [ perim, uncorr_perim ] = perimeter3d( o )
-%PERIMETER3D Perimeter of a closed N-dimensional polygon.
-
-    perim = compute_perim( o.boundary );
-    uncorr_perim = compute_perim( o.boundary( : , 1:2 ) );
-
-    %% Subfunction
-    
-    function l_perim = compute_perim( p )
-    %   p can be a N x d matrix, with d being the dimensionality.
-
-        p2 = [ p ; p( 1, : ) ];
-        p_diff = diff( p2 );
-
-        p_diff_2 = p_diff .* p_diff;
-        p_diff_2_sum  = sum( p_diff_2, 2 );
-        sls = sqrt( p_diff_2_sum );
-        l_perim = sum( sls );
-
-    end
-
-end
-